Rounds of BQSR in GATK3 GenericPreProcessingWorkflow
I reviewed the GATK3 WDL Preprocessing workflow on gitHub, and found something strange.
I recall in GATK3, we'd need to run BQSR twice, then use PrintReads to apply the results of BQSR. However, it seemed the code only runs BQSR once before running PrintReads. Can anyone confirm that we actually need to run it twice? Thanks!